Thanks for the reply, Panda.
I haven't adjusted any of the config files, only changed the starting perks for units. I also didn't save/load during the mission. The hover casualties pop-up displayed normal numbers. I can't tell you the exactly, but there were small numbers, like 30 killed and 100 wounded.
But, I have another clue. When I replayed the mission, I got this issue again (even bigger vet pool,around 3k). After that I decided to delete save games that I had (the last was after CSA Gaines Mill, and my army was in poor condition). It worked, the bug hasn't occured anymore.
I also thought that high casialties of the command unit could cause the issue (it was tanking some shots during the battle), but after I deleted saves it worked just fine.
So probably it is something with saves, the only thing that comes to mind.